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AlexsLemonade / alsf-scpca

Management and analysis tools for ALSF Single-cell Pediatric Cancer Atlas data.
BSD 3-Clause "New" or "Revised" License
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Create reference files and indexes #3

Closed jashapiro closed 4 years ago

jashapiro commented 4 years ago

All mapping workflows will require reference files and accompanying indexes. To create these, we will use a Nextflow workflow.

This workflow should download all necessary reference files (hg38 sequence, GTF, etc.), storing them in s3://ccdl-nextflow-data/reference. My current preference is to download these reference files from Ensembl, and group all files by Ensembl version.

These should then be indexed for both salmon and kallisto. For salmon, we will start with the simplest index of just the cDNA, with the potential to add decoy-aware mapping in the future.

jashapiro commented 4 years ago

I am going to consider this done when the basic steps are completed in #6 and #7. More focused issues for later steps are in #11 and #12

jashapiro commented 4 years ago

Considering this closed by #7, specific extensions in other issues, as, noted: https://github.com/AlexsLemonade/alsf-scpca/issues/3#issuecomment-677801813